Monday, April 29, 2019

For those interested in and working with
1) new technological and bioinformatic approaches to detecting and differentiating intestinal parasites
2) the role of Blastocystis and other common luminal intestinal parasitic protists
there are currently a few interesting calls:

Mark van der Giezen (with whom I've had the pleasure of working with on a couple of projects) recently tweeted:

Moving on to special issues in journals, I would like to highlight that Parasite Epidemiology and Control (PEC) is planning to publish two special issues of particular interest to our community:

Special Issue: 2nd International Blastocystis Conference

As the readers of this blog will know, the 2nd International Blastocystis Conference took place in Bogotá, Colombia only half a year ago. A special issue in PEC will be dedicated to this conference. It welcomes papers on Blastocystis also from those of our colleagues who could not attend the conference. You can read more here.

Special Issue: Novel Technologies and Approaches for Detecting Intestinal Parasites
Together with Juan David Ramirez Gonzalez I look very much forward to editing a special issue on new technologies and approaches to detecting intestinal parasites. I'm thinking metagenomics, amplicon-based sequencing, etc. Of course, also papers describing non-DNA-based methods are welcome. You can read more here.

Special Issue: Recent Advances in the Controverisal Human Pathogens Pneumocystis, Microsporidia, and Blastocystis

Finally, I'd like to highlight a special issue call from Frontiers in Microbiology on Pneumocystis, microsporidia, and Blastocystis - the odd ones out. Please go here for more information. The special issue is edited by Olga Matos, Lihua Xiao, and myself.

The online journal 'Frontiers in Microbiology - Infectious Diseases' will be publishing a special issue on Blastocystis, Pneumocystis and microsporidia as opportunistic eukaryotes and controversial pathogens.

Friday, December 21, 2018

The 2nd International Blastocystis Conference was so much more than a worthy sequel to the conference in Ankara in 2015, - it was also the conference that initiated the tradition of having a conference on Blastocystis every three years! And as most of you probably know, the next conference will be in Crete in 2021. More info to follow.

We also had a specific Blastocystis session in ICOPA 2018 in Daegu, South Korea, and I expect that this is also something that we'll see more of in future conferences.

Most exciting Blastocystis-related paper of the year for me is probably the one published by Raul Tito and colleagues in the journal Gut, which is available for free download here. The paper is a good example of the opportunity we have to study Blastocystis across geographical regions and taxonomic kingdoms. I would very much like to re-congratulate Raul on his fantastic work! His work sets an example for all of us.

Everyone, please remember that we have founded the International Blastocystis Network, which is a memeber of World Federation of Parasitology. Please help us come up with ideas as to what it can be used for.

To those of you who celebrate Christmas: Happy Christmas!
And a Happy New Year to everyone!

Blastocystis is a species complex and as such, it is difficult to generalize on its roles in health and disease.

Studies are revealing that
intra-subtype variations are associated with different phenotypes, so it is
likely that we will require more resolution (allelic) when studying the effects
of Blastocystis on the host.

Recent metagenomics studies
on stools of healthy individuals associate the presence of Blastocystis with
a diverse bacterial microbiota, but more studies are required on diseased
groups to identify their possible associations with rare/ pathogenic isolates
(e.g. ST7 isolates).

Recent work on rodent models
are shedding light on possible pathogenic effects of acute Blastocystis infections.

More studies on the cell
and molecular biology of Blastocystis are required to better understand
the molecular basis for Blastocystis-host interactions (identify virulence
factors, adaptation strategies etc).

It is very likely that more surprises are in store for the curious and observant Blastocystis researcher!

We shouldn’t try to generalize about characteristics of
‘Blastocystis’ based on studies of individual isolates. This is a
category error — Blastocystis comprises many many different organisms with
different genetic makeups. There is variation not just between subtypes,
but within subtypes. So we shouldn’t say “Blastocystis is a
commensal/parasite” because different Blastocystis isolates could be
commensals or parasites depending on the host, the genetic makeup of the
parasite and the microbiota with which they interact.

In microbiome studies, colonization with Blastocystis
in general seems to correlate with a different composition of the prokaryotic
microbiota in hosts.

We know virtually NOTHING about the basic cell biology
of Blastocystis (Kevin Tan’s group is making important inroads into
understanding this).

We know virtually NOTHING about how Blastocystis
interacts with (or responds to) other microbes and the host immune system.

There may be an important impact of host diet on
Blastocystis colonization and ‘behaviour'.

The diversity of Blastocystis in humans and animals is
huge — new lineages are being continuously revealed.

Friday, October 19, 2018

So, a lot of people would like to know about the take-home messages from the recent 2nd International Blastocystis Conference in Bogotá. There were many, and I might develop one more post to make room for more.

The first - and most important - thing I'd like to emphasise is that the community interested in Blastocystis is growing. And we're seeing a clearly multidisciplinary approach to studying the parasite. I think that this is what we need. The initial ideas about having Blastocystis-specific conference were developed by Funda Dogruman-Al and myself, and we both have a background in clinical microbiology. We have realised that in order to make sense of Blastocystis in a clinical microbiology (and infectious disease) context, we need research input from bordering fields, such as biology (genomics, cell biology, etc.), veterinary medicine (host specificity and impact of Blastocystis on animal health), gastroenterology (connection to microbiota and the extent of Blastocystis being involved in functional and inflammatory bowel diseases), bioinformatics (processing NGS data such as those pertaining to the profiling of gut microbiota communities), and ecology (people who are used to study interactions between organisms). At the conference, I believe that all (or at least most) of these fields were represented.

I was also thrilled to realise that many researchers have now adapted to the subtype terminology, - and even the allele terminology appears to be useful and pragmatic.

Status on the Blastocystis genome project. Slide by Andrew Roger.

Andrew Roger highlighted that the genomes of Blastocystis are
more different than the genomes of human and mouse! Well-annotated
genomes are available for ST1, ST4, and ST7, while draft genomes are
available for subtypes 2, 3, 6, 8 and 9.

What use are genomes? Summary provided by Andrew Roger.

Animal experimental modelling is possible. We know that rats can be colonised/infected by Blastocystis ST1 strain from a human and shed cysts in stool for more than one year.

Blastocystis is one of the few parasites that are really easy to culture and easy to get by. If we can learn to induce cysts in culture, these can be separated by sucrose gradient centrifugation or other methods and used for inoculation into volunteers, pigs, or rats, for instance. This can be used to study the impact of Blastocystis on the host, including immune system and gut microbiota. Baseline microbiota profiling is necessary prior to inoculation to know about the background variation in study individuals.

In terms of Blastocystis and gut microbiota: Since we published our conspicuous observations in 2015, many researchers have now corroborated our findings:Blastocystis is typically linked to increased microbiota richness and diversity; - something, which is generally considered a benefit and which is linked not only to gut health, but also to leanness. Especially the negative association between Blastocystis and Bacteroides has been highlighted by many now. It will be very interesting to learn why this is so. It also seems that Blastocystis are more common in individuals with a gut microbiota dominated by strictly anaerobes rather than facultative aerobes.Faecal microbiota transplantaion (FMT): The recommendation of excluding FMT donors based on the finding of Blastocystis came up many times and was discussed in the context of the microbiota studies. It appear relevant to investigate further whether FMT donors should really be dismissed if they are Blastocystis-positive.

Some of the take home messages from Raul Tito Tadeo's talk.

In many animal groups, Blastocystis is a very common finding. These include mostly omnivores or herbivores. On the contrary, Blastocystis is very rare in strict carnivores, with no consistency in subtype distribution, indicating that these animals are not natural hosts of Blastocystis.The Blastocystis incidentially found in these hosts might stem from the prey that they have eaten.

Finally, I wish to highlight that there are excellent resources available from the pre-conference workshop, including an R script for microbiota analysis, and some tools for Blastocystis genome annotation. Please visit my previous blog post for links to these.

We cannot totally dismiss pathogenicity of Blastocystis; if existing, it may involve both strain- and host-specific factors.

And.... it's out: The time and venue for the 3rd International Blastocystis Conference will be Crete in 2021 (possibly June), with Eleni Gentekaki and Anastasios Tsaousis being involved in both the scientific and local organising committees... ! Please mark you calendars!

We are all very thankful to Juan-David and his colleagues, the entire LOC, the Universidad del Rosario in Bogotá and La Fontana Hotel, which provided an excellent framework with premium facilities.

The Faculty can be seen on the image below. From left to right, it's Rodolfo Casero, [Magdalena Maria Martinez Agüero, Director of Investigation and Innovation, Facultad de Ciencias Naturales Y Matemáticas, Universidad del Rosario], Andrew Roger, Rune Stensvold, Hisao Yoshikawa, Raul Tito Tadeo, Monica Santin-Duran, Funda Dogruman-Al, Kevin Tan, and Juan David Ramirez Gonzalez. Workshop sessions and keynote lectures were developed and given by members of the Faculty.

The workshop took place on 9–10 October and covered sessions on diagnosis (microscopy, culture, PCR, etc.), in vivo and in vitro experimental models, subtype calling from DNA sequence data, gut microbiota analysis (NGS data processing in R), genomics and evolution (introduction to Blastocystis genomics and resources available), and theoretical topics linked to epidemiology, clinical microbiology and infectious disease issues.

Some of the workshop participants and Faculty members

The conference took place on 11–12 October and consisted of nine keynote lectures delivered by the Faculty members, 12 oral presentations and 22 poster presentations.

The award for the best oral presentation was given to Justinn Hamilton who is an ecologist now based at University of Copenhagen for his talk 'Exploring interactions between Blastocystis sp., other intestinal parasites and the gut microbiomes of wild Chimpanzees (Senegal): Not-so-friendly old-friends-hypothesis'.

The award for the best poster presentation went to David Carmena's group for the impressive study 'Molecular epidemiology of Blastocystis sp. in asymptomatic school children from Madrid, Spain'.

The workshop programme can be viewed/downloaded here, and the conference programme is available here. The poster programme is available here.
Please go here to browse conference proceedings, and here for workshop guidelines.
Stay tuned for Wrap Up Part II and III, which will include more photos and some of the take-home messages from the conference.

Monday, October 1, 2018

Need I remind you that the 2nd International Blastocystis Conference is just around the corner!

You can find an updated list of speakers and the entire programme here.

It will be a total of 4 (f-o-u-r!!) days of discussion of Blastocystis research and sharing of experience in terms of e.g. diagnostics, typing, and genome sequencing.

We'll be covering most areas, including clinical and public health significance, host specificity, genetic diversity, genomics, metagenomics/amplicon-based sequencing, Blastocystis in the clinical microbiology setting, etc. And of course there will be a lot of survey data.

Tuesday, July 10, 2018

Three months until kick-off of 2nd International Blastocystis Conference in Bogotá!

A couple of updates:

Abstract submission deadline has been postponed to 15th of August 2018.

We have had a couple of speaker cancellations. Drs Pauline Scanland and Katerina Pomajbikova will not be able to participate. Hopefully, we'll be blessed by their presence at the next big Blasto event. Instead, Drs Raul Tito-Tadeo and Hisao Yoshikawa have very kindly accepted to give keynote lectures and lead workshop sessions. And so we will still have a great event!

For more information on workshop and conference, please visit the official conference website here.

Since it's summer here in Europe, and since I love Phlox, I thought,
I'd attach a couple of images that I received yesterday from my dear friend
Jaco Verweij.

Tuesday, July 3, 2018

Experimental models are critical to advancing our knowledge on the role of Blastocystis in health and disease.

We have now published our work led by Dr Katerina Pomajbikova on the suitability of the rat as a model of Blastocystis colonisation. We observed that the rats were able to sustain the colonisation for more than one year, when a ST1 strain isolated from a human was used.

Next step could now be to monitor gut microbiota before and after challenge with Blastocystis cysts and look for changes at both individual and community level,, changes in alpha and beta diversity, etc.

Friday, June 22, 2018

There's only little more than three months before the kick-off of our 2nd International Blastocystis Conference! And as in the case of our 1st conference in Ankara in 2015, participants are in for a real treat! I simply don't know where to begin... !

Well, for starters, here's the hotel in which the conference will take place (11–12 October). It's the Hotel Estelar La Fonata in Bogotá! I think it looks amazing!

Please go to the conference website and find more information: http://www.urosario.edu.co/Blastocystis/en/home/

The line-up of faculty members is impressive; again, please visit website to update yourself with workshop leaders and keynote speakers.

We will be dealing with anything from diagnostics to genomics, from epidemiology to cell biology, from experimental models to phylogenetics!

There will be plenty of Colombian coffee to sample and you might also with to sign up for the gala dinner!

So, don't miss out on the opportunity to put yourself into the very epicentre of Blastocystis research and experience the dynamic city of Bogotá!

Importantly, the deadline for abstract submission is 1st of July, so pleaseeveryone: Get your act together - submit your abstract today and support us with your presence and your enthusiasm with regard to the most common parasite in the human gut: Blastocystis!

Wednesday, March 21, 2018

As an appropriate follow-up on yesterday's post, I feel like guiding your attention to the paper by Laforest-Lapointe and Arrieta from University of Calgary, Canada with the title 'Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies', which elaborates on some of the issues that we have already been highlighting several times in the past.

Nevermind, in their article, which just appeared in the ASM-based journal "mSystems", they speculate that the reason for the observed link between Blastocystis colonisation and increased bacterial diversity (which was mentioned several times in the paper that I referred to yesterday) might be due to predation by Blastocystis on bacteria, a process which selects for higher diversity. They argue that

"In the absence of Blastocystis, a strong bacterial competitor dominates the community, which limits species richness and community evenness; when [Blastocystis is] present, its predation on abundant bacterial taxa lowers the competition for nutrients and space, which leads to an increase in bacterial richness and community evenness."

Since predation on bacteria by Blastocystis has only been documented once (I believe) to date, the authors are right in encouraging colleagues to study engulfment of bacteria by Blastocystis.

Those of us who take a special interest in the public health impact of common intestinal parasites and who work in the field of clinical microbiology and infectious diseases might benefit from taking some lessons from experts in 'food web theory' and micro- and macroecology.

Tuesday, March 20, 2018

For those interested in exploring the presence/absence of intestinal parasites in a gut microbiome context, Dr Mark van der Giezen and I did this small opinion paper for Trends in Parasitology. In it, we summarize data from studies looking at the associations between single-celled intestinal (luminal) parasites and gut bacteria, and we tried to come up with a hypothesis for the factors governing the presence/absence of e.g. Blastocystis.

Wednesday, February 21, 2018

I have a potential PhD position available for a suitable candidate on the impact of antibiotics on gut microbiome diversity and function - check out the link to my site for more information! Please Retweet! https://t.co/GzqI2A2UwF

Friday, October 13, 2017

Thanks to Juan-David Ramirez Gonzales and his colleauges, the official poster for the 2nd International Blastocystis Conference is now available.

I put it on Google Drive as a pdf file, which you can download here. Please share it on facebook. Please also print it and use it to adorn your institutes, hospital departments, offices, canteens, homes, etc... Thanks!

Monday, July 31, 2017

I thought I'd post two current conference abstracts to exemplify some of the trends in Blastocystis research.

The first is from Dr Pauline D Scanlan, who will be speaking at 15th International Congress of Protistology currently taking place in Prague. Go herefor more info about the meeting.

In the symposium 'The eukaryome, bringing protists into the spotlight of microbiome research' taking place today, Pauline will be giving a talk with the title:

Inter-Kingdom Interactions in the human gut microbiome-the
prevalence of the intestinal protist Blastocystis
is linked to host age, antibiotic use and gut bacterial diversity and composition

and the abstract reads like this:

The
human gut is host to a complex microbial ecosystem that plays a central role in
host health. In addition to bacteria, viruses and archaea, the gut microbiota includes
a diversity of fungal and protist species that are collectively referred to as
the gut ‘eukaryome’. Although research into the gut eukaryome is in its infancy,
emerging data indicates that the intestinal protist Blastocystis is perhaps the most common member of the human gut
eukaryome worldwide. Despite its association with intestinal disease, asymptomatic
carriage is common with Blastocystis frequently
observed in surveys of the healthy adult gut microbiome. Furthermore, Blastocystis is less prevalent in chronic
diseases such as Irritable Bowel Syndrome compared to healthy controls.
Antibiotic administration significantly reduces Blastocystis prevalence rates between case and controls groups with
the reduction in Blastocystis
prevalence in the antibiotic treated group possibly due to direct effects on Blastocystis and/or secondary loss due
to loss of bacteria that Blastocystis
interacts with. In support of this latter hypothesis, data showing correlations
between the presence of Blastocystis
and specific features of the bacterial component of the gut microbiome (high diversity
and a specific bacterial composition) are suggestive of inter-kingdom
interactions between bacteria and Blastocystis
in the gut microbiome. Blastocystis
is less prevalent in infant populations relative to contemporaneous adult populations
indicating that Blastocystis is not adapted
to the infant gut. Given the difference in microbiome composition and diversity
in infants compared to adults perhaps Blastocystis
requires a more adult-like gut microbiome for successful colonisation.
Collectively, emerging data suggests that successful colonisation of the gut by
Blastocystis is linked to the composition
and diversity of the bacterial fraction of human gut microbiome. Consequently, interactions
between Blastocystis and bacteria in
the gut microbiome may account for some of the variation in prevalence rates
observed across age, health and geography.

Along similar lines, I will be giving a talk at the EMBO conference 'Anaerobic protists: Integrating Parasitology with mucosal microbiota and immunology' running from 31 AUG to 03 SEP in Newcastle, UK. You can read about the conference here.

The title and abstract of my talk are as follows:

The diversity of the most common intestinal protists, Blastocystis and Dientamoeba, and their interactions with the microbiota: what role in health and disease?

The integration of DNA-methods in
Clinical Microbiology has enabled a more detailed and accurate snapshot of the
protists colonising and infecting our guts. Parasites like Blastocystis and Dientamoeba
are much more common than previously known, when detection relied mainly on
microscopy of faecal concentrates and smears only.

While Dientamoeba isolated from humans exhibits very little genetic
variation across the small subunit ribosomal gene, Blastocystis displays a perplexing amount of genetic heterogeneity,
and nine subtypes, which are arguably separate species, have been found in
humans. Subtypes 1 to 4 account for about 95% of human Blastocystis carriage.

It is expected that over 1 billion
people are colonised by Blastocystis,
and based on DNA-based detection, prevalence figures of up to 100% have been
reported in developing countries. Conversely, the prevalence of Blastocystis appears relatively low in
e.g. the US, and it has been suggested that the low prevalence is indicative of
the defaunation of indviduals adapting a Westernized life style.

In a developed country like Denmark, the
prevalence of Blastocystis and Dientamoeba is highest in individuals
without gastrointestinal, while the prevalence of these parasites is lower in
patients with functional and organic bowel disease, suggesting that these
parasites are in fact markers of gastrointestinal health.

This is also in part exemplified by
recent independent data linking high gut microbiota diversity to the presence
of these parasites. Certain bacterial populations appear to be linked to
parasite carriage, and studies are emerging that try to look into the
association between these parasites and the remaining gut microbiota.

Moreover, higher age appears to be
linked to Blastocystis colonisation. Blastocystis is more common in older
children and adults, while in younger children, Dientamoeba is much more common.

Whether these parasites are able to
modulate gut microbiota structure and function remains unknown, and it also
remains to be demonstrated whether certain microbiota communities and/or
metabolites are required for successful establishment of these parasites. More
research data on these topics will inform future advances in probiotics in
particular and gut microbiota manipulation in general.

Thoughts on Blastocystis in Amazon

On Blastocystis

Blastocystis is a protist parasitising the intestine of humans and a variety of animals. We estimate that at least 1 billion people worldwide are colonised by this parasite, most of whom probably experience no more episodes of intestinal upset, e.g. diarrhoea, than the average individual. In any case, many people have Blastocystis wihtout knowing and without feeling sick. Blastocystis may colonise the intestine for a long time (i.e. months or years).Many species of Blastocystis have been acknowledged, of which at least 9 have been found in humans. Such species are currently termed "subtypes" (STs). ST1, ST2, ST3 and ST4 are common in Europe. While ST1, ST2, and ST3 appear to have equal prevalences in patients with diarrhoea and healthy individuals, ST4 appears to be epidemiologically linked to diarrhoea and/or chronic conditions such as irritable bowel syndrome (IBS).

There is no known efficient eradication strategy for Blastocystis. Although metronidazole is often prescribed for Blastocystis infections, there is conflicting reports on its efficacy. Even in combination with a luminal agent, such as paromomycin, Blastocystis eradication cannot be guaranteed. Read more here.

I'm very interested in studies aiming to explore1) Blastocystis in the environment2) Why some people are colonised while others are not3) Whether Blastocystis colonisation requires a certain intestinal flora (e.g. enterotype) to establish4) To which extent human Blastocystis is acquired from animal reservoirs5) Potential differences in virulence between subtypes or strains (by for instance comparative genomic studies)

During my Blastocystis research, I and my colleagues have discovered/developed1) New Blastocystis species2) Precise molecular methods for accurate detection (PCR)3) High resolution typing systems (MLST) for strain identification of Blastocystis4) A standardised nomenclature for Blastocystis5) A publicly available database for identification of subtypes and sequence data despository (please see links below)

Using microscopy-, culture-based and molecular tools we have generated data that have shed light over the transmission and distribution of Blastocystis subtypes in human and animals.